| Column number: Node in JAR3D model: Insertion positions indicated by I: Position in motif group: | 1 1 I | 2 2 1 | 3 2 I | 4 3 2 | 5 4 I | 6 5 3 | 7 6 I | 8 9 4 | 9 9 I | 10 10 | 11 9 I | 12 9 5 | 13 8 I | 14 12 6 | 15 13 I | 16 16 7 | 17 16 I | 18 17 | 19 16 I | 20 16 8 | 21 15 I | 22 19 9 | 23 20 I | 24 21 10 | 25 22 I | 26 23 11 | 27 24 I | 28 25 12 | 29 26 I | 30 27 13 | 31 27 I | 32 28 | 33 27 I | 34 27 14 | 35 2 I | 36 2 15 | 37 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J4_22413.2_Instance_1 J4_22413.2,J4_1U0B_001,U7_A66 | U | U | A | A | U | A | G | U | C | U | A | G | U | A | A | |||||||||||||||||||||||||||
| J4_22413.2_Sequence_1 J4_22413.21U0B_U7_A66 | U | U | A | A | * | U | A | G | * | U | C | U | A | G | U | * | A | A | true | 89 | 0 | 0 | 2.17 | |||||||||||||||||||
| J4_22413.2_Instance_2 J4_22413.2,J4_2IY5_001,G7_C66 | G | U | A | G | C | A | U | A | G | U | G | U | C | C | G | C | ||||||||||||||||||||||||||
| J4_22413.2_Sequence_2 J4_22413.22IY5_G7_C66 | G | U | A | G | * | C | A | U | * | A | G | U | G | U | C | C | * | G | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||||
| J4_22413.2_Instance_3 J4_22413.2,J4_5WT1_002,G7_C66 | G | U | A | G | C | A | C | G | G | U | G | U | C | G | C | C | ||||||||||||||||||||||||||
| J4_22413.2_Sequence_3 J4_22413.25WT1_G7_C66 | G | U | A | G | * | C | A | C | * | G | G | U | G | U | C | G | * | C | C | true | 100 | 0 | 0 | 0.00 |
1 13 s35 1 15 cWW 3 11 s55 4 5 cWW 4 6 s55 4 10 cHW 5 6 s35 6 7 s35 7 8 cWW 13 14 cWW 13 15 s55 14 15 s35 11 3 2BPhJAR3D SCFG/MRF model for J4_22413.2:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [15] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009408334,0.019174796,0.010588934,0.197715832,0.000000000],[0.018564311,0.009546870,0.199060083,0.012415910,0.000000000],[0.010514048,0.221541448,0.002054132,0.025278139,0.000000000],[0.208398617,0.012527047,0.033081112,0.010130387,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [15] // Basepair U7 - A66 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | Position [1] | Left Index [2] | Right Index [14] // Fixed node on left for 1U0B|1|A|U|8 InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [14] // Fixed node on left for 1U0B|1|A|A|9 InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [14] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [4] | Right Index [14] // Junction node A10 - A65 ID J8491 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009490394,0.020648938,0.010590347,0.209997349,0.000000000],[0.017070363,0.009463878,0.198130626,0.012189443,0.000000000],[0.010502710,0.222275070,0.002053109,0.035235925,0.000000000],[0.195916611,0.012742798,0.023085133,0.010607307,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // Basepair A10 - U25 cWW HairpinNode | Num Bases [1] | Left Index [5] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node type * Interaction | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [14] // Initial node 1U0B|1|A|A|26 - 1U0B|1|A|A|65 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [6] | Right Index [14] // Fixed node on left for 1U0B|1|A|A|26 InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [14] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [7] | Right Index [14] // Junction node G27 - A65 ID J9339 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.011358885,0.109438110,0.011616510,0.158345366,0.000000000],[0.018499668,0.010673294,0.155740043,0.012953173,0.000000000],[0.011562281,0.144944442,0.002435587,0.132159202,0.000000000],[0.155733715,0.013004573,0.031182208,0.020352945,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // Basepair G27 - U43 cWW HairpinNode | Num Bases [1] | Left Index [8] | Right Index [8] | Norm Constant [1.000000000000000] // Hairpin node type * Interaction | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [14] // Initial node 1U0B|1|A|C|44 - 1U0B|1|A|A|65 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.300000000,0.500000000,0.100000000,0.000000000] | Position [1] | Left Index [9] | Right Index [14] // Fixed node on left for 1U0B|1|A|C|44 InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | Position [1] | Left Index [10] | Right Index [14] // Fixed node on left for 1U0B|1|A|U|45 InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [11] | Right Index [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.326086957,0.021739130,0.630434783,0.021739130,0.000000000] | Position [1] | Left Index [11] | Right Index [14] // Fixed node on left for 1U0B|1|A|A|46 InitialNode | Left Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Left Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [12] | Right Index [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.500000000,0.300000000,0.100000000,0.000000000] | Position [1] | Left Index [12] | Right Index [14] // Fixed node on left for 1U0B|1|A|G|48 InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [13] | Right Index [14] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009343268,0.018128250,0.010549122,0.196880225,0.000000000],[0.019613658,0.009602282,0.210732508,0.012583150,0.000000000],[0.010555512,0.209899895,0.002054288,0.024189159,0.000000000],[0.209264206,0.012361836,0.034173856,0.010068786,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [13] | Right Index [14] // Basepair U49 - A65 cWW HairpinNode | Num Bases [1] | Left Index [14] | Right Index [14] | Norm Constant [1.000000000000000] // Hairpin node type * Interaction | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncationSequences of instances from J4_22413.2:
> J4_22413.2 1U0B U 7 A 66 UUAA*UAG*UCUAGU*AA > J4_22413.2 2IY5 G 7 C 66 GUAG*CAU*AGUGUCC*GC > J4_22413.2 5WT1 G 7 C 66 GUAG*CAC*GGUGUCG*CC